update namespace, news

DESCRIPTION

@@ -35,7 +35,9 @@ Imports:
     RaMS,
     tibble,
     xml2,
-    bit64
+    bit64,
+    data.table,
+    base64enc
 Suggests: 
     entab,
     ncdf4,

NAMESPACE

@@ -38,12 +38,14 @@ importFrom(RaMS,grabMSdata)
 importFrom(bit64,as.integer64)
 importFrom(bitops,bitAnd)
 importFrom(bitops,bitShiftL)
+importFrom(data.table,.SD)
 importFrom(purrr,partial)
 importFrom(readxl,read_xls)
 importFrom(stats,reshape)
 importFrom(stringr,str_split_fixed)
 importFrom(utils,file_test)
 importFrom(utils,head)
+importFrom(utils,packageVersion)
 importFrom(utils,read.csv)
 importFrom(utils,read.table)
 importFrom(utils,tail)

NEWS.md

@@ -1,25 +1,36 @@
 ## chromConverter 0.7.0
 
-### New parsers
+### Major features
 
 * Added preliminary support for 'Varian Worktation' (`.sms`) format through `read_varian_sms` function.
 * Added preliminary support for 'Shimadzu QGD' GCMS files through the `read_shimadzu_qgd` function.
-* Added preliminary support for 'Allotrope Simple Model' (ASM) chromatography date files. 
+* Added preliminary support for 'Allotrope Simple Model' (ASM) 2D chromatography date files.
+* Added option to write mzML files (MS1 and DAD).
+
+### UI changes
+
+* Changed order of arguments in `read_chroms` so that `format_in` comes second after `path`.
+* Removed extraneous `export` argument from `read_chroms`. To export files, you now only need to provide an argument to `export_format`.
+* Updated handling of multiple chromatograms by `read_shimadzu_lcd`. The function now returns a list of named chromatograms if `data_format == "wide"` and returns multiple chromatograms in a single `data.frame` if `data_format == "long"`.
+* Added `scale` argument to `read_chemstation_uv` and `read_shimadzu_ascii` to toggle scaling of chromatograms.
+* Harmonized file path arguments across parser functions by changing `file` arguments to `path`.
+* Harmonized column names in output across parsers.
+* Small changes in `read_cdf` UI: `what` now defaults to `NULL` and defaults are coded into downstream `read_andi_chrom` and `read_andi_ms` functions.
 
 ### Other improvements
 
+* Added `data.table` as an option for `format_out`.
 * Improved speed of `read_shimadzu_lcd` by dealing with twos-complements more sensibly.
-* Updated handling of multiple chromatograms by `read_shimadzu_lcd`. The function now returns a list of named chromatograms if `data_format == "wide"` and returns multiple chromatograms in a single `data.frame` if `data_format == "long"`.
 * Start 'Shimadzu LCD' chromatogram retention times at dwell time (DLT).
 * Give temp files generated from Shimadzu OLE files informative names.
-* Added `scale` argument to `read_chemstation_uv` and `read_shimadzu_ascii` to toggle scaling of chromatograms.
 * Use 'Output Date' field instead of 'Type' to find 'Shimadzu' ASCII delimiter. (This seems to be a more generalizable solution since some files do not contain the 'Type' field).
-* Harmonized file path arguments across parser functions by changing `file` arguments to `path`.
 * Allow relative paths for `path_out` when using 'ThermoRawFileParser' and 'OpenChrom' parsers.
 * Allow creation of new directories by `read_chroms` if `path_out` does not exist.
 * Fixed bug affecting some `mdf` files lacking null bytes after the file header.
 * Eliminated 'magrittr' dependency by using xpath to parse XML in a more straightforward fashion.
 * Fixed bug causing truncation of sample names at the first period by `read_chroms`.
+* Modified `export_csv` function to label first column for wide-format chromatograms.
+* Improved handling of metadata from rainbow parsers.
 
 ## chromConverter 0.6.4